Problems compiling aliBuild "flpproto" target under SLC7

aferrero · November 30, 2018, 6:50pm

Dear all,

I am trying to build the flpproto target with aliBuild on a standard SLC7 system, but the compilation gets stuck when building O2, with the following error:

Scanning dependencies of target test_MCHContour_Edge
Scanning dependencies of target test_MCHContour_ContourCreator
[  1%] Building CXX object Detectors/MUON/MCH/Contour/CMakeFiles/test_MCHContour_ContourCreator.dir/test/ContourCreator.cxx.o
[  1%] Building CXX object Detectors/MUON/MCH/Contour/CMakeFiles/test_MCHContour_Edge.dir/test/Edge.cxx.o
Scanning dependencies of target test_MCHContour_Interval
[  1%] Building CXX object Detectors/MUON/MCH/Contour/CMakeFiles/test_MCHContour_Interval.dir/test/Interval.cxx.o
[  1%] Building CXX object DataFormats/Headers/CMakeFiles/Headers.dir/src/NameHeader.cxx.o
[  1%] Building CXX object DataFormats/Headers/CMakeFiles/Headers.dir/src/HeartbeatFrame.cxx.o
input_line_12:3656:10: fatal error: 'TPCFastTransform.h' file not found
#include "TPCFastTransform.h"
         ^~~~~~~~~~~~~~~~~~~~
Error: /root/alice/sw/slc7_x86-64/ROOT/v6-14-04-1/bin/rootcint: compilation failure (/root/alice/sw/BUILD/79cf4da209480d4a3a19856d0bb4b938628f7f24/O2/Detectors/TPC/reconstruction/TPCCAGPUTracking/G__O2TPCCAGPUTrackingDicte00050bad9_dictUmbrella.h)
gmake[2]: *** [Detectors/TPC/reconstruction/TPCCAGPUTracking/G__O2TPCCAGPUTrackingDict.cxx] Error 1
gmake[1]: *** [Detectors/TPC/reconstruction/TPCCAGPUTracking/CMakeFiles/O2TPCCAGPUTracking.dir/all] Error 2
gmake[1]: *** Waiting for unfinished jobs....

Here are the steps I followed to setup the aliBuild environment:

pip install alibuild --upgrade

export ALIBUILD_WORK_DIR="$HOME/alice/sw"
export PATH=/opt/alisw/el7/Python/v2.7.10-36/bin:$PATH
eval "`alienv shell-helper`"

aliBuild init QualityControl@master --default o2
aliBuild build flpproto --default o2

Any idea?

Thanks a lot in advance!

bvonhall · December 3, 2018, 8:21am

Dear Andrea,
Sorry about that.
Not sure what is going on (yet).

First, I would get rid of this line. Even though it will not fix your problem :
export PATH=/opt/alisw/el7/Python/v2.7.10-36/bin:$PATH
CC7 comes with a python that should be ok.

Second, could you run aliDoctor and let me know what is the output ?

Third, did you install devtoolset ?

Four, I think that you can safely use the defaults o2-dataflow as you don’t need the simulation packages.

Five, could you do

cd <build dir of O2> 
make VERBOSE=1

Cheers,
Barth

aferrero · December 3, 2018, 10:30am

At some point I had to set this variable because otherwise the system was picking aliBuild from /usr/bin. This morning this folder is already included in the PATH when running

aliswmod enter flpproto/v0.9.2-4

No idea what was wrong last week…

I have re-compiled the code with --default o2-dataflow, and now I can proceed up to the QualityControl target, where I get this new error:

CMake Error at Framework/CMakeLists.txt:74 (get_target_property):
  get_target_property() called with non-existent target "AliceO2::Common".

Here is the full cmake log:

+ case $ARCHITECTURE in
+ rsync -a --ignore-existing /root/alice/sw/slc7_x86-64/CodingGuidelines/master-1/.clang-format /root/alice/sw/SOURCES/QualityControl/master/0
+ cmake /root/alice/sw/SOURCES/QualityControl/master/0 -DCMAKE_INSTALL_PREFIX=/root/alice/sw/slc7_x86-64/QualityControl/master-1 -DBOOST_ROOT=/root/alice/sw/slc7_x86-64/boost/v1.68.0-1 -DCommon_ROOT=/root/alice/sw/slc7_x86-64/Common-O2/v1.3.0-1 -DConfiguration_ROOT=/root/alice/sw/slc7_x86-64/Configuration/v2.2.0-1 -DInfoLogger_ROOT=/root/alice/sw/slc7_x86-64/InfoLogger/v1.0.9-1 -DO2_ROOT=/root/alice/sw/slc7_x86-64/O2/fc3f879f67_O2_DATAFLOW-1 -DFAIRROOTPATH=/root/alice/sw/slc7_x86-64/FairRoot/c672f280ec-1 -DFairRoot_DIR=/root/alice/sw/slc7_x86-64/FairRoot/c672f280ec-1 -DMS_GSL_INCLUDE_DIR=/root/alice/sw/slc7_x86-64/ms_gsl/1-1/include -DARROW_HOME=/root/alice/sw/slc7_x86-64/arrow/v0.10.0-alice1-1 -DCMAKE_CXX_STANDARD=17 -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
-- The CXX compiler identification is GNU 7.3.0
-- Check for working CXX compiler: /opt/alisw/el7/GCC-Toolchain/v7.3.0-alice1-3/bin/c++
-- Check for working CXX compiler: /opt/alisw/el7/GCC-Toolchain/v7.3.0-alice1-3/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


CMake Warning at /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:839 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:950 (_Boost_COMPONENT_DEPENDENCIES)
  /root/alice/sw/slc7_x86-64/CMake/v3.11.0-1/share/cmake-3.11/Modules/FindBoost.cmake:1618 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:72 (find_package)


-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   container
--   unit_test_framework
--   program_options
--   system
--   log
--   signals
--   system
--   date_time
--   log_setup
--   filesystem
--   thread
--   regex
--   chrono
--   atomic
-- Configuration 1.5.2 found
-- Monitoring 1.9.2 found
-- Found MySQL: /usr/lib64/mysql/libmysqlclient.so
-- Found Common: /root/alice/sw/slc7_x86-64/Common-O2/v1.3.0-1/lib/libCommon.so  
-- Common found : /root/alice/sw/slc7_x86-64/Common-O2/v1.3.0-1/lib/libCommon.so
-- Found InfoLogger: /root/alice/sw/slc7_x86-64/InfoLogger/v1.0.9-1/lib/libInfoLogger.so  
-- InfoLogger found : /root/alice/sw/slc7_x86-64/InfoLogger/v1.0.9-1/lib/libInfoLogger.so
-- Found AliceO2: /root/alice/sw/slc7_x86-64/O2/fc3f879f67_O2_DATAFLOW-1/lib/libFramework.so  
-- AliceO2 found, libraries: /root/alice/sw/slc7_x86-64/O2/fc3f879f67_O2_DATAFLOW-1/lib/libFramework.so;/root/alice/sw/slc7_x86-64/O2/fc3f879f67_O2_DATAFLOW-1/lib/libHeaders.so;/root/alice/sw/slc7_x86-64/O2/fc3f879f67_O2_DATAFLOW-1/lib/libCCDB.so;/root/alice/sw/slc7_x86-64/O2/fc3f879f67_O2_DATAFLOW-1/lib/libDebugGUI.so
-- Found CURL: /usr/lib64/libcurl.so (found version "7.29.0") 
-- Looking for ZeroMQ
-- Looking for ZeroMQ - Found /root/alice/sw/slc7_x86-64/ZeroMQ/v4.1.5-1/include
-- Looking for ZeroMQ - Found version 4.1.5
-- Arrow include path: /root/alice/sw/slc7_x86-64/arrow/v0.10.0-alice1-1/include
-- Found the Arrow library: /root/alice/sw/slc7_x86-64/arrow/v0.10.0-alice1-1/lib/libarrow.so
-- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so
-- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /usr/lib64/libX11.so
-- Could NOT find GLFW (missing: GLFW_INCLUDE_DIR GLFW_LIBRARIES) 
-- Setting FairRoot environment…
-- FairRoot ... - found /root/alice/sw/slc7_x86-64/FairRoot/c672f280ec-1
-- FairRoot Library directory  :     /root/alice/sw/slc7_x86-64/FairRoot/c672f280ec-1/lib
-- FairRoot Include path…      :     /root/alice/sw/slc7_x86-64/FairRoot/c672f280ec-1/include
-- FairRoot Cmake Modules      :     /root/alice/sw/slc7_x86-64/FairRoot/c672f280ec-1/share/fairbase/cmake
-- Found ROOT: /root/alice/sw/slc7_x86-64/ROOT/v6-14-04-1/cmake/ROOTConfig.cmake (found suitable version "6.14.04", minimum required is "6.06.02") 
CMake Error at Framework/CMakeLists.txt:74 (get_target_property):
  get_target_property() called with non-existent target "AliceO2::Common".


-- GLFW not found, DataDump will not be built
CMake Error at cmake/QCModulesUtils.cmake:51 (get_target_property):
  get_target_property() called with non-existent target "AliceO2::Common".
Call Stack (most recent call first):
  Modules/Common/CMakeLists.txt:34 (generate_root_dict)


CMake Error at cmake/QCModulesUtils.cmake:51 (get_target_property):
  get_target_property() called with non-existent target "AliceO2::Common".
Call Stack (most recent call first):
  Modules/Daq/CMakeLists.txt:38 (generate_root_dict)


CMake Error at cmake/QCModulesUtils.cmake:51 (get_target_property):
  get_target_property() called with non-existent target "AliceO2::Common".
Call Stack (most recent call first):
  Modules/Example/CMakeLists.txt:40 (generate_root_dict)


CMake Error at cmake/QCModulesUtils.cmake:51 (get_target_property):
  get_target_property() called with non-existent target "AliceO2::Common".
Call Stack (most recent call first):
  Modules/Skeleton/CMakeLists.txt:38 (generate_root_dict)


-- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") found components:  doxygen dot 
-- Configuring incomplete, errors occurred!
See also "/root/alice/sw/BUILD/2caa15f273148fc1544f1b1183e2aae5e7f591eb/QualityControl/CMakeFiles/CMakeOutput.log".
See also "/root/alice/sw/BUILD/2caa15f273148fc1544f1b1183e2aae5e7f591eb/QualityControl/CMakeFiles/CMakeError.log".

And here is the output of aliBuild doctor flpproto --default o2-dataflow:

SUCCESS: Package GCC-Toolchain will be picked up from the system.
WARNING: Package boost cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING: 
WARNING: brew() { true; }; printf "#include \"boost/version.hpp\"\n# if (BOOST_VERSION < 106800 || BOOST_VERSION > 106899)\n#error \"Cannot use system's boost: boost 1.68 required.\"\n#endif\nint main(){}" | gcc -I$(brew --prefix boost)/include -xc++ - -o /dev/null
WARNING: 
WARNING: with the following output:
WARNING: 
WARNING: boost: <stdin>:3:2: error: #error "Cannot use system's boost: boost 1.68 required."
WARNING: boost: 
WARNING: 
WARNING: Package CMake cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING: 
WARNING: brew() { true; }; which cmake && case `cmake --version | sed -e 's/.* //' | cut -d. -f1,2,3 | head -n1` in [0-2]*|3.[0-9].*|3.10.*) exit 1 ;; esac
WARNING: 
WARNING: with the following output:
WARNING: 
WARNING: CMake: /usr/bin/cmake
WARNING: CMake: 
WARNING: 
SUCCESS: Required package curl will be picked up from the system.
WARNING: Package Vc cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING: 
WARNING: brew() { true; }; printf "#include <Vc/version.h>\n#if Vc_VERSION_CHECK(1,3,2) > Vc_VERSION_NUMBER\n#error Incorrect Vc version\n#endif" | c++ -xc++ - -c -M 2>&1
WARNING: 
WARNING: with the following output:
WARNING: 
WARNING: Vc: <stdin>:1:10: fatal error: Vc/version.h: No such file or directory
WARNING: Vc: compilation terminated.
WARNING: Vc: 
WARNING: 
SUCCESS: Required package MySQL will be picked up from the system.
WARNING: Package node cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING: 
WARNING: brew() { true; }; node -h &> /dev/null || { echo "node is missing"; exit 1; }
WARNING: if [[ $(printf "%d%04d%04d" $(node --version | sed -e 's/v//g; s/\./ /g')) -le 900090000 ]]; then echo "higher node version required"; exit 1; fi
WARNING: 
WARNING: with the following output:
WARNING: 
WARNING: node: node is missing
WARNING: node: 
WARNING: 
SUCCESS: Package Python-modules will be picked up from the system.
SUCCESS: Package libpng will be picked up from the system.
SUCCESS: Package lzma will be picked up from the system.
SUCCESS: Required package bz2 will be picked up from the system.
SUCCESS: Package zlib will be picked up from the system.
WARNING: Package flatbuffers cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING: 
WARNING: brew() { true; }; printf "#include \"flatbuffers/flatbuffers.h\"\nint main(){}" | c++ -I$(brew --prefix flatbuffers)/include -xc++ -std=c++11 - -o /dev/null
WARNING: 
WARNING: with the following output:
WARNING: 
WARNING: flatbuffers: <stdin>:1:10: fatal error: flatbuffers/flatbuffers.h: No such file or directory
WARNING: flatbuffers: compilation terminated.
WARNING: flatbuffers: 
WARNING: 
WARNING: Package protobuf cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING: 
WARNING: brew() { true; }; printf "#include \"google/protobuf/stubs/common.h\"\n#if (GOOGLE_PROTOBUF_VERSION < 3000000)\n#error \"At least protobuf 3.0.0 is required.\"\n#endif\nint main(){}" | c++ -I$(brew --prefix protobuf)/include -Wno-deprecated-declarations -xc++ - -o /dev/null && protoc -h &> /dev/null
WARNING: 
WARNING: with the following output:
WARNING: 
WARNING: protobuf: <stdin>:1:10: fatal error: google/protobuf/stubs/common.h: No such file or directory
WARNING: protobuf: compilation terminated.
WARNING: protobuf: 
WARNING: 
WARNING: Package ZeroMQ cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING: 
WARNING: brew() { true; }; printf "#include <zmq.h>\n#if(ZMQ_VERSION < 40105)\n#error \"zmq version >= 4.1.5 needed\"\n#endif\n int main(){}" | gcc -I$(brew --prefix zeromq)/include $([[ -d $(brew --prefix zeromq) ]] || echo "-l:libzmq.a") -xc++ - -o /dev/null 2>&1
WARNING: 
WARNING: with the following output:
WARNING: 
WARNING: ZeroMQ: <stdin>:1:10: fatal error: zmq.h: No such file or directory
WARNING: ZeroMQ: compilation terminated.
WARNING: ZeroMQ: 
WARNING: 
WARNING: Package nanomsg cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING: 
WARNING: brew() { true; }; printf "#include \"nanomsg/nn.h\"\nint main(){}" | cc -I$(brew --prefix nanomsg)/include -Wno-deprecated-declarations -xc - -o /dev/null
WARNING: 
WARNING: with the following output:
WARNING: 
WARNING: nanomsg: <stdin>:1:10: fatal error: nanomsg/nn.h: No such file or directory
WARNING: nanomsg: compilation terminated.
WARNING: nanomsg: 
WARNING: 
WARNING: Package msgpack cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING: 
WARNING: brew() { true; }; printf "#include <msgpack/version.hpp>\n#define VERSION (MSGPACK_VERSION_MAJOR * 10000) + (MSGPACK_VERSION_MINOR * 100) + MSGPACK_VERSION_REVISION\n#if(VERSION < 20105)\n#error \"msgpack version >= 2.1.5 needed\"\n#endif\nint main(){}" | c++ -I$(brew --prefix msgpack)/include -xc++ -std=c++11 - -o /dev/null
WARNING: 
WARNING: with the following output:
WARNING: 
WARNING: msgpack: <stdin>:1:10: fatal error: msgpack/version.hpp: No such file or directory
WARNING: msgpack: compilation terminated.
WARNING: msgpack: 
WARNING: 
SUCCESS: Required package kernel-devel will be picked up from the system.
SUCCESS: Package autotools will be picked up from the system.
SUCCESS: Required package motif will be picked up from the system.
WARNING: Package GSL cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING: 
WARNING: brew() { true; }; printf "#include \"gsl/gsl_version.h\"\n#define GSL_V GSL_MAJOR_VERSION * 100 + GSL_MINOR_VERSION\n# if (GSL_V < 116)\n#error \"Cannot use system's gsl. Notice we only support versions from 1.16 (included)\"\n#endif\nint main(){}" | gcc  -I$(brew --prefix gsl)/include -xc++ - -o /dev/null
WARNING: 
WARNING: with the following output:
WARNING: 
WARNING: GSL: <stdin>:1:10: fatal error: gsl/gsl_version.h: No such file or directory
WARNING: GSL: compilation terminated.
WARNING: GSL: 
WARNING: 
SUCCESS: Required package opengl will be picked up from the system.
SUCCESS: Required package Xdevel will be picked up from the system.
SUCCESS: Package FreeType will be picked up from the system.
SUCCESS: Package libxml2 will be picked up from the system.
SUCCESS: Package OpenSSL will be picked up from the system.

==> The following packages will be picked up from the system:
    
    - Python-modules
    - lzma
    - FreeType
    - libxml2
    - zlib
    - OpenSSL
    - GCC-Toolchain
    - libpng
    - autotools
    
    If this is not you want, you have to uninstall / unload them.

==> The following packages will be built by aliBuild because they couldn't be picked up from the system:
    
    - node
    - Vc
    - CMake
    - protobuf
    - flatbuffers
    - msgpack
    - nanomsg
    - ZeroMQ
    - boost
    - GSL
    
    This is not a real issue, but it might take longer the first time you invoke aliBuild.
    Look at the error messages above to get hints on what packages you need to install separately.

bvonhall · December 3, 2018, 10:45am

aferrero:

At some point I had to set this variable because otherwise the system was picking aliBuild from /usr/bin. This morning this folder is already included in the PATH when running
aliswmod enter flpproto/v0.9.2-4
No idea what was wrong last week…

I would be careful mixing the RPMs installed software and the alibuild software, i.e. aliswmod (RPM) and alienv (alibuild). I would not run aliswmod in the terminal in which I work with alibuild.

I will come back with some proposals for the QC error. This is something I should be able to help with.

Cheers,
Barth

aferrero · December 3, 2018, 11:29am

I am trying this just now, will let you know how it goes…

aferrero · December 3, 2018, 5:46pm

Tried compiling in a “clean” environment, still the same:

-- Found ROOT: /root/alice/sw/slc7_x86-64/ROOT/v6-14-04-1/cmake/ROOTConfig.cmake (found suitable version "6.14.04", minimum required is "6.06.02") 
CMake Error at Framework/CMakeLists.txt:74 (get_target_property):
  get_target_property() called with non-existent target "AliceO2::Common".

bvonhall · December 4, 2018, 8:31am

Ok, I am releasing a new version of QC that hopefully will fix the problem. I’ll let you know when it is ready.

bvonhall · December 4, 2018, 1:06pm

There is a new version of QC. Please update alidist (git pull in alidist) and then run aliBuild. Let’s see if it helps.

bvonhall · December 5, 2018, 7:52am

Also, if you update alibuild (sudo pip install alibuild --upgrade) , the new version will download directly precompiled packages instead of building them locally on your machine.

aferrero · December 5, 2018, 10:23am

Hi!

after updating alibuild and deleting the alienist folder (so that it got re-created from scratch) the QC now compiles fine!

Now I can start experimenting with the QC framework.

Thanks a lot!

bvonhall · December 5, 2018, 11:27am

Thank you for your undestanding and patience.

aferrero · December 19, 2018, 1:11pm

@bvonhall
I am again encountering problems to compile the QualityControl target, this time due to errors during ROOT dictionary generation:

++ cmake --build . -- -j7 install
[  1%] Generating QualityControlDict.cxx, libQualityControlDict_rdict.pcm, libQualityControlDict.rootmap
In file included from input_line_12:9:
In file included from /root/alice/sw/SOURCES/QualityControl/master/0/Framework/include/QualityControl/Checker.h:15:
In file included from /root/alice/sw/slc7_x86-64/Configuration/v2.2.0-1/include/Configuration/ConfigurationInterface.h:13:
In file included from /root/alice/sw/slc7_x86-64/boost/v1.68.0-1/include/boost/property_tree/ptree.hpp:16:
In file included from /root/alice/sw/slc7_x86-64/boost/v1.68.0-1/include/boost/property_tree/string_path.hpp:16:
In file included from /root/alice/sw/slc7_x86-64/boost/v1.68.0-1/include/boost/property_tree/exceptions.hpp:17:
In file included from /root/alice/sw/slc7_x86-64/boost/v1.68.0-1/include/boost/any.hpp:20:
In file included from /root/alice/sw/slc7_x86-64/boost/v1.68.0-1/include/boost/type_index.hpp:29:
In file included from /root/alice/sw/slc7_x86-64/boost/v1.68.0-1/include/boost/type_index/stl_type_index.hpp:42:
In file included from /root/alice/sw/slc7_x86-64/boost/v1.68.0-1/include/boost/container_hash/hash.hpp:114:
/root/alice/sw/slc7_x86-64/GCC-Toolchain/v7.3.0-alice1-8/bin/../lib/gcc/x86_64-unknown-linux-gnu/7.3.0/../../../../include/c++/7.3.0/variant:238:46: error: cannot cast 'const std::variant<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, o2::framework::data_matcher::ContextRef>' to its private base class 'std::__detail::__variant::_Variant_storage<false, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, o2::framework::data_matcher::ContextRef>'
      return __get(std::in_place_index<_Np>, std::forward<_Variant>(__v)._M_u);
                                             ^
/root/alice/sw/slc7_x86-64/GCC-Toolchain/v7.3.0-alice1-8/bin/../lib/gcc/x86_64-unknown-linux-gnu/7.3.0/../../../../include/c++/7.3.0/variant:800:31: note: in instantiation of function template specialization 'std::__detail::__variant::__get<1, const std::variant<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, o2::framework::data_matcher::ContextRef> &>' requested here
        return &__detail::__variant::__get<_Np>(*__ptr);
                                     ^
/root/alice/sw/slc7_x86-64/GCC-Toolchain/v7.3.0-alice1-8/bin/../lib/gcc/x86_64-unknown-linux-gnu/7.3.0/../../../../include/c++/7.3.0/variant:822:14: note: in instantiation of function template specialization 'std::get_if<1, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, o2::framework::data_matcher::ContextRef>' requested here
      return get_if<__detail::__variant::__index_of_v<_Tp, _Types...>>(__ptr);
             ^
/root/alice/sw/slc7_x86-64/O2/5af9cc38f2_O2_DATAFLOW-1/include/../include/Framework/DataDescriptorMatcher.h:196:25: note: in instantiation of function template specialization 'std::get_if<o2::framework::data_matcher::ContextRef, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, o2::framework::data_matcher::ContextRef>' requested here
    if (auto ref = std::get_if<ContextRef>(&mValue)) {                        ^

As far as I can tell, all my O2 dependencies are up-to-date.

Any idea? Thanks!

bvonhall · December 19, 2018, 3:19pm

Hi,
There is ticket here : https://alice.its.cern.ch/jira/browse/QC-131
The problem is probably not in QC , at least it has been traced back to a PR in O2.
I would propose to go back to a stable commit in O2 : cd O2; git checkout 74b986

Sorry about the inconvenience. I thought that we built the whole O2Suite upon PRs in O2. It is apparently not the case yet.

aferrero · January 8, 2019, 2:18pm

Looks like this problem is finally solved!

bvonhall · January 8, 2019, 2:26pm

Yes ! sorry about that and thank you for your patience.